docs: the handbook follows the three layers: swarm, hives, agents

The handbook's sections were agent-lifecycle, integrations, swarm, tools,
trust-boundary and web-ui, which do not follow how the system is built, so a
reader could not tell which layer a page is about. Its pages now sit in
swarm/, hives/ and agents/, with the accounts an agent can hold outside the
system in external-accounts/.

- swarm/: forge, matrix and the knowledge repo join the swarm pages, and so
  does the swarmctl reference.
- hives/: the dashboard, hivectl and its reference, and the operator/agent
  boundary, with a README that takes over the old web-ui and tools pages.
- agents/: the roster, persistence, config changes, the agent's own web page
  (was web-ui/agent) and the security model, with a README.
- external-accounts/: GitHub and GitLab.

Pages are moved whole; none is split yet. Every reference follows: relative
links in the docs, `docs/2-handbook/...` paths in code comments, the nix
checks that regenerate the CLI references and the ignore list, and docs/README.md,
whose handbook section is now by layer.

frontend/packages/agent/src/screen.html

@@ -36,7 +36,7 @@
     <script>
       // Minimal RFB-over-WebSocket renderer. Connects to `screen/ws` on
       // the same host; the harness relays raw RFB bytes to the VNC server
-      // running inside the container. See docs/2-handbook/web-ui/agent.md (GET /screen)
+      // running inside the container. See docs/2-handbook/agents/web-page.md (GET /screen)
       // for the design rationale + canvas-sizing implementation notes.
 
       (function () {
@@ -61,7 +61,7 @@
         });
 
         // --- Fit-to-window toggle ---
-        // See docs/2-handbook/web-ui/agent.md::Per-agent endpoints (GET /screen) for the
+        // See docs/2-handbook/agents/web-page.md::Per-agent endpoints (GET /screen) for the
         // localStorage persistence + canvas-intrinsic-resolution +
         // pointer-rescale model.
         let fitMode = localStorage.getItem("screen-fit") !== "off";
@@ -105,7 +105,7 @@
         // Sends an RFB SetDesktopSize request so the VNC server (weston)
         // changes its actual output resolution to match the browser
         // viewport — sharper than fit-mode's CSS downscale. Gated on the
-        // server's ExtendedDesktopSize advert; see docs/2-handbook/web-ui/agent.md::Per-agent
+        // server's ExtendedDesktopSize advert; see docs/2-handbook/agents/web-page.md::Per-agent
         // endpoints (GET /screen).
         let extDesktopSupported = false;
         let screenId = 1; // captured from the server's ExtendedDesktopSize advert